rs7550106

Variant names:

• chr1-152224726-T-C
• rs7550106
• ENST00000420707.5:n.159-24169T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-152224726-T-C
• chr1-152224726-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420707.5(CCDST):​n.159-24169T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,080 control chromosomes in the GnomAD database, including 37,181 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (37181 hom., cov: 32)
• Consequence: CCDST ENST00000420707.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 4 publications found

Genes affected

CCDST (HGNC:55988): (cervical cancer associated DHX9 suppressive transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDST	NR_186761.1	n.354-24169T>C		intron_variant	Intron 1 of 7
CCDST	NR_186762.1	n.179+35245T>C		intron_variant	Intron 1 of 5
CCDST	NR_186763.1	n.206+35218T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDST	ENST00000420707.5	n.159-24169T>C		intron_variant	Intron 1 of 8	5
CCDST	ENST00000593011.5	n.296+56306T>C		intron_variant	Intron 1 of 3	4
CCDST	ENST00000630125.3	n.179+35245T>C		intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102492 AN: 151962 Hom.: 37159 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.681

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.674 AC: 102541 AN: 152080 Hom.: 37181 Cov.: 32 AF XY: 0.667 AC XY: 49604 AN XY: 74344

African (AFR) AF: 0.441 AC: 18271 AN: 41448

American (AMR) AF: 0.597 AC: 9115 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2359 AN: 3470

East Asian (EAS) AF: 0.373 AC: 1928 AN: 5172

South Asian (SAS) AF: 0.563 AC: 2711 AN: 4818

European-Finnish (FIN) AF: 0.816 AC: 8634 AN: 10576

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57136 AN: 68000

Other (OTH) AF: 0.685 AC: 1446 AN: 2110

Alfa AF: 0.718 Hom.: 14016

Bravo AF: 0.649

Asia WGS AF: 0.439 AC: 1528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.73
PhyloP100		0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7550106; hg19: chr1-152197202;